Ubiquitin-like protein SMT3
Saccharomyces cerevisiae
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain A； UniProt 1–101 | Not recorded | No other associated polymer | SOLUTION NMR NMR measurement conditions：pH 6.5；293 K；Pressure 1 NMR sample composition：1 mM C13 and 15N Labelled | 90% H2O/10% D2O | Resolution not provided |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 1L2N | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 11HK SARS-CoV-2 spike S2 trimer stabilized in the early fusion intermediate conformation (E-FICs-v3) bound to the VN01H1 Fab (Fab local refinement) Deposited 2026-02-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–94（94 aa）
Chain D
1–94（94 aa）
Chain G
1–94（94 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 11HL SARS-CoV-2 spike S2 trimer stabilized in the early fusion intermediate conformation (E-FICs-v3) bound to the VN01H1 Fab (S2 local refinement) Deposited 2026-02-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–94（94 aa）
Chain B
1–94（94 aa）
Chain C
1–94（94 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 11HN SARS-CoV-2 spike S2 trimer stabilized in the early fusion intermediate conformation (E-FICs-v3) bound to C77G12 (S2 local refinement) Deposited 2026-02-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–94（94 aa）
Chain B
1–94（94 aa）
Chain C
1–94（94 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 11HW SARS-CoV-2 spike S2 trimer stabilized in the early fusion intermediate conformation (E-FICs-v3) bound to C77G12 (Fab local refinement) Deposited 2026-02-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–94（94 aa）
Chain B
1–94（94 aa）
Chain G
1–94（94 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 1EUV X-RAY STRUCTURE OF THE C-TERMINAL ULP1 PROTEASE DOMAIN IN COMPLEX WITH SMT3, THE YEAST ORTHOLOG OF SUMO. Deposited 2000-04-17 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
13–98（86 aa）
Fragment：SMT3 RESIDUES 13-98
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1M MES pH6.5, 10% w/v polyethylene glycol 20000, 3% w/v 1,6-hexandiol, VAPOR DIFFUSION, HANGING DROP, temperature 294K
|
Resolution 1.60 Å R-free 0.251 |
| 2EKE Structure of a SUMO-binding-motif mimic bound to Smt3p-Ubc9p: conservation of a noncovalent Ubiquitin-like protein-E2 complex as a platform for selective interactions within a SUMO pathway Deposited 2007-03-23 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
13–98（86 aa）
|
Mutation：thrombin site, Ubiquitin-like | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；18% PEG 3350, 0.2M magnesium chloride, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.250 |
| 2EKE Structure of a SUMO-binding-motif mimic bound to Smt3p-Ubc9p: conservation of a noncovalent Ubiquitin-like protein-E2 complex as a platform for selective interactions within a SUMO pathway Deposited 2007-03-23 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
13–98（86 aa）
|
Mutation：thrombin site, Ubiquitin-like | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；18% PEG 3350, 0.2M magnesium chloride, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.250 |
| 3PGE Structure of sumoylated PCNA Deposited 2010-11-01 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–98（98 aa）
Fragment：sumo-C fragment of PCNA
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；2.0M Ammonium Sulfate, 0.1M sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.80 Å R-free 0.253 |
| 3QHT Crystal Structure of the Monobody ySMB-1 bound to yeast SUMO Deposited 2011-01-26 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–98（97 aa）
|
Not recorded | GOL GLYCEROL × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8；292 K；14% PEG8000, 16% glycerol, pH 8.0, VAPOR DIFFUSION, temperature 292K
|
Resolution 2.40 Å R-free 0.272 |
| 3QHT Crystal Structure of the Monobody ySMB-1 bound to yeast SUMO Deposited 2011-01-26 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–98（97 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8；292 K；14% PEG8000, 16% glycerol, pH 8.0, VAPOR DIFFUSION, temperature 292K
|
Resolution 2.40 Å R-free 0.272 |
| 3TIX Crystal structure of the Chp1-Tas3 complex core Deposited 2011-08-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
3–98（96 aa）
Fragment：N-TERMINAL DOMAIN,N-TERMINAL DOMAIN
|
Not recorded | CL CHLORIDE ION × 4 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.2；290 K；microseeding in 0.95 M potassium sodium tartrate, 100 mM MES, 180 mM sodium thiocyanate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K
|
Resolution 2.90 Å R-free 0.243 |
| 3TIX Crystal structure of the Chp1-Tas3 complex core Deposited 2011-08-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
3–98（96 aa）
Fragment：N-TERMINAL DOMAIN,N-TERMINAL DOMAIN
|
Not recorded | CL CHLORIDE ION × 4 K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.2；290 K；microseeding in 0.95 M potassium sodium tartrate, 100 mM MES, 180 mM sodium thiocyanate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K
|
Resolution 2.90 Å R-free 0.243 |
| 3UF8 Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase with a G95A surface mutation from Burkholderia pseudomallei complexed with FK506 Deposited 2011-10-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–98（86 aa）
Fragment：Q12306 residues 13-98, Q3JK38 residues 2-113
|
Mutation：G95A | FK5 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；290 K；Internal tracking number 226425. JCSG well A8. 0.2M Ammonium Formate, 20.0% w/v PEG3500, PEG400 Cryo. BupsA.00130.a.D242 PD00198 21.4mg/ml, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K
|
Resolution 1.50 Å R-free 0.183 |
| 3UQA Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase with surface mutation A54E from Burkholderia pseudomallei complexed with FK506 Deposited 2011-11-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–98（86 aa）
Fragment：Q12306 residues 13-98, Q3JK38 residues 2-113
|
Mutation：A54E | FK5 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN × 1 PEG DI(HYDROXYETHYL)ETHER × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；290 K；Internal tracking number 226422. JCSG well A9. 0.2M Ammonium Chloride, 20.0% w/v PEG3500, 30% PEG400 Cryo. BupsA.00130.a.D220 PD00197 19.3mg/ml., pH 7.00, vapor diffusion, sitting drop, temperature 290K
|
Resolution 1.55 Å R-free 0.193 |
| 3UQB Crystal structure of a SMT Fusion PEPTIDYL-PROLYL CIS-TRANS ISOMERASE with surface mutation D44G from Burkholderia pseudomallei complexed with FK506 Deposited 2011-11-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–98（86 aa）
Fragment：Q12306 residues 13-98, Q3JK38 residues 2-113
|
Mutation：D44G | FK5 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 9；290 K；Internal tracking number 226421. PACT well B6. 0.1M MIB Buffer pH 9.0, 25.0% w/v PEG1500, 30% PEG400 Cryo. BUPSA.00130.A.D214 PD00190/6 23.7mg/ml, vapor diffusion, sitting drop, temperature 290K, VAPOR DIFFUSION, SITTING DROP
|
Resolution 1.90 Å R-free 0.228 |
| 3V60 Structure of S. cerevisiae PCNA conjugated to SUMO on lysine 164 Deposited 2011-12-18 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
20–98（79 aa）
Fragment：unp resicues 20-98
|
Not recorded | SO4 SULFATE ION × 18 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；291 K；4% PEG 8000, 500 mM LiSO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.60 Å R-free 0.249 |
| 3V61 Structure of S. cerevisiae PCNA conjugated to SUMO on lysine 164 Deposited 2011-12-18 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
20–98（79 aa）
Fragment：unp residues 20-98
|
Not recorded | BA BARIUM ION × 13 NEQ N-ETHYLMALEIMIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；21% MPD, 100 mM BaCl2, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.80 Å R-free 0.254 |
| 3V62 Structure of the S. cerevisiae Srs2 C-terminal domain in complex with PCNA conjugated to SUMO on lysine 164 Deposited 2011-12-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
20–98（79 aa）
Fragment：unp residues 20-98
|
Mutation：GSH from N-tag after thrombin cleavage, K19R Non-standard monomer：Yes (specific site not provided by mmCIF) | NEQ N-ETHYLMALEIMIDE × 2 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；279 K；1.9 M AMMONIUM SULFATE
4% PEG 400
100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K
|
Resolution 2.90 Å R-free 0.237 |
| 3V62 Structure of the S. cerevisiae Srs2 C-terminal domain in complex with PCNA conjugated to SUMO on lysine 164 Deposited 2011-12-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
20–98（79 aa）
Fragment：unp residues 20-98
|
Mutation：GSH from N-tag after thrombin cleavage, K19R Non-standard monomer：Yes (specific site not provided by mmCIF) | NEQ N-ETHYLMALEIMIDE × 2 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；279 K；1.9 M AMMONIUM SULFATE
4% PEG 400
100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K
|
Resolution 2.90 Å R-free 0.237 |
| 3VAW Crystal structure of a smt fusion peptidyl-prolyl cis-trans isomerase with surface mutation v3i from burkholderia pseudomallei complexed with fk506 Deposited 2011-12-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–99（87 aa）
Fragment：Q12306 RESIDUES 13-99, Q3JK38 RESIDUES 2-113
|
Mutation：V3I,V3I | FK5 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；Internal tracking number 226593. PACT well H3. 0.2M Sodium Iodide, 0.1M Bis-Tris Propane, pH 8.5, 20.0% w/v PEG3350, 30% PEG400 Cryo. BupsA.00130.a.D24 PD00194 19.6mg/ml., vapor diffusion, sitting drop, temperature 290K
|
Resolution 1.55 Å R-free 0.194 |
| 4FN2 Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase with surface mutation D44G from Burkholderia pseudomallei complexed with CJ37 Deposited 2012-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–98（86 aa）
Fragment：Q12306 residues 13-98, Q3JK38 residues 2-113
|
Mutation：D44G | 854 ethyl (2S)-1-(benzylsulfonyl)piperidine-2-carboxylate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；Internal tracking number 233926b1. Puck VKT6-6, Morpheus well B1. 10% PEG 20,000, 20% PEG MME550, 0.03M Halides (NaF, NaBr, NaI), 0.1M MES/Imidazole pH 6.5, Direct Cryo. BupsA.00130.a.D214, 20.00 mg/ml, CJ37 (EBSI2854), vapor diffusion, sitting drop, temperature 295K
|
Resolution 1.95 Å R-free 0.224 |
| 4FN2 Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase with surface mutation D44G from Burkholderia pseudomallei complexed with CJ37 Deposited 2012-06-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–98（86 aa）
Fragment：Q12306 residues 13-98, Q3JK38 residues 2-113
|
Mutation：D44G | 854 ethyl (2S)-1-(benzylsulfonyl)piperidine-2-carboxylate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；Internal tracking number 233926b1. Puck VKT6-6, Morpheus well B1. 10% PEG 20,000, 20% PEG MME550, 0.03M Halides (NaF, NaBr, NaI), 0.1M MES/Imidazole pH 6.5, Direct Cryo. BupsA.00130.a.D214, 20.00 mg/ml, CJ37 (EBSI2854), vapor diffusion, sitting drop, temperature 295K
|
Resolution 1.95 Å R-free 0.224 |
| 4G50 Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase with surface mutation D44G from Burkholderia pseudomallei complexed with CJ168 Deposited 2012-07-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–98（86 aa）
Fragment：Q12306 residues 13-98, Q3JK38 residues 2-113
|
Mutation：D44G | 861 3-(3,4,5-trimethoxyphenyl)propyl (2S)-1-(benzylsulfonyl)piperidine-2-carboxylate × 1 FMT FORMIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；Internal tracking number 233897a9. Puck VKT6-9, JCSG_A8 optimization. 50mM Ammonium formate, 24.55% PEG 3,350, 10% ethylene glycol. BupsA.00130.a.D214, 20.00 mg/ml, CJ168 (EBSI2861), pH 7.5, vapor diffusion, sitting drop, temperature 295K
|
Resolution 1.75 Å R-free 0.219 |
| 4G50 Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase with surface mutation D44G from Burkholderia pseudomallei complexed with CJ168 Deposited 2012-07-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–98（86 aa）
Fragment：Q12306 residues 13-98, Q3JK38 residues 2-113
|
Mutation：D44G | 861 3-(3,4,5-trimethoxyphenyl)propyl (2S)-1-(benzylsulfonyl)piperidine-2-carboxylate × 1 FMT FORMIC ACID × 2 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；Internal tracking number 233897a9. Puck VKT6-9, JCSG_A8 optimization. 50mM Ammonium formate, 24.55% PEG 3,350, 10% ethylene glycol. BupsA.00130.a.D214, 20.00 mg/ml, CJ168 (EBSI2861), pH 7.5, vapor diffusion, sitting drop, temperature 295K
|
Resolution 1.75 Å R-free 0.219 |
| 4GGQ Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei complexed with CJ40 Deposited 2012-08-07 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
13–98（86 aa）
Fragment：Q12306 residues 13-98, Q3JK38 residues 2-113
|
Not recorded | CA CALCIUM ION × 1 861 3-(3,4,5-trimethoxyphenyl)propyl (2S)-1-(benzylsulfonyl)piperidine-2-carboxylate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；Internal tracking number 235051a1. Puck IBH5-4, Morpheus well A1. 10% PEG 20,000, 20% PEG MME550, 0.03M Divalent Catios (MgCl2, CaCl2), 0.1M MES/Imidazole pH 6.5, Direct Cryo. BupsA.00130.a.D21, 20.00 mg/ml, CJ40 (EBSI2855), vapor diffusion, sitting drop, temperature 295K
|
Resolution 1.95 Å R-free 0.220 |
| 4GGQ Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei complexed with CJ40 Deposited 2012-08-07 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–98（86 aa）
Fragment：Q12306 residues 13-98, Q3JK38 residues 2-113
|
Not recorded | CA CALCIUM ION × 1 861 3-(3,4,5-trimethoxyphenyl)propyl (2S)-1-(benzylsulfonyl)piperidine-2-carboxylate × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；Internal tracking number 235051a1. Puck IBH5-4, Morpheus well A1. 10% PEG 20,000, 20% PEG MME550, 0.03M Divalent Catios (MgCl2, CaCl2), 0.1M MES/Imidazole pH 6.5, Direct Cryo. BupsA.00130.a.D21, 20.00 mg/ml, CJ40 (EBSI2855), vapor diffusion, sitting drop, temperature 295K
|
Resolution 1.95 Å R-free 0.220 |
| 4GGQ Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei complexed with CJ40 Deposited 2012-08-07 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–98（86 aa）
Fragment：Q12306 residues 13-98, Q3JK38 residues 2-113
|
Not recorded | 861 3-(3,4,5-trimethoxyphenyl)propyl (2S)-1-(benzylsulfonyl)piperidine-2-carboxylate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；Internal tracking number 235051a1. Puck IBH5-4, Morpheus well A1. 10% PEG 20,000, 20% PEG MME550, 0.03M Divalent Catios (MgCl2, CaCl2), 0.1M MES/Imidazole pH 6.5, Direct Cryo. BupsA.00130.a.D21, 20.00 mg/ml, CJ40 (EBSI2855), vapor diffusion, sitting drop, temperature 295K
|
Resolution 1.95 Å R-free 0.220 |
| 4GGQ Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei complexed with CJ40 Deposited 2012-08-07 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
13–98（86 aa）
Fragment：Q12306 residues 13-98, Q3JK38 residues 2-113
|
Not recorded | 861 3-(3,4,5-trimethoxyphenyl)propyl (2S)-1-(benzylsulfonyl)piperidine-2-carboxylate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；Internal tracking number 235051a1. Puck IBH5-4, Morpheus well A1. 10% PEG 20,000, 20% PEG MME550, 0.03M Divalent Catios (MgCl2, CaCl2), 0.1M MES/Imidazole pH 6.5, Direct Cryo. BupsA.00130.a.D21, 20.00 mg/ml, CJ40 (EBSI2855), vapor diffusion, sitting drop, temperature 295K
|
Resolution 1.95 Å R-free 0.220 |
| 4GIV Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase with surface mutation D44G from Burkholderia pseudomallei complexed with CJ183 Deposited 2012-08-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–98（86 aa）
Fragment：Q12306 residues 13-98, Q3JK38 residues 2-113
|
Mutation：D44G | 4GI 3-(pyridin-3-yl)propyl (2S)-1-[(3-nitrophenyl)sulfonyl]piperidine-2-carboxylate × 1 FMT FORMIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；Internal tracking number 232625a12. Puck IBH5-9, JCSG_A8 optimization screen. 50mM Ammonium Formate, 30% PEG3,350, 25% ethylene glycol cryo-protected. BupsA.00130.a.D214, 20.00 mg/ml, CJ183 (EBSI2864), pH 7.5, vapor diffusion, sitting drop, temperature 295K
|
Resolution 2.45 Å R-free 0.262 |
| 4GIV Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase with surface mutation D44G from Burkholderia pseudomallei complexed with CJ183 Deposited 2012-08-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–98（86 aa）
Fragment：Q12306 residues 13-98, Q3JK38 residues 2-113
|
Mutation：D44G | 4GI 3-(pyridin-3-yl)propyl (2S)-1-[(3-nitrophenyl)sulfonyl]piperidine-2-carboxylate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；Internal tracking number 232625a12. Puck IBH5-9, JCSG_A8 optimization screen. 50mM Ammonium Formate, 30% PEG3,350, 25% ethylene glycol cryo-protected. BupsA.00130.a.D214, 20.00 mg/ml, CJ183 (EBSI2864), pH 7.5, vapor diffusion, sitting drop, temperature 295K
|
Resolution 2.45 Å R-free 0.262 |
| 5D6J Crystal structure of a mycobacterial protein Deposited 2015-08-12 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
21–94（74 aa）
Fragment：UNP RESIDUES 21-94
|
Not recorded | MG MAGNESIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；281 K；0.2 M sodium malonate, 20% PEG 3350
|
Resolution 2.25 Å R-free 0.206 |
| 5JNE E2-SUMO-Siz1 E3-SUMO-PCNA complex Deposited 2016-04-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
20–98（79 aa）
Fragment：unp residues 167-445
Chain C
19–98（80 aa）
|
Mutation：Siz1 C361D, Smt3 Delta N-terminus 1-18 Mutation：N-terminal 1-18 delete, K19R | ZN ZINC ION × 1 GOL GLYCEROL × 6 6LN ethane-1,2-dithiol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1 M Tris-HCl (pH 8.5), 5% PEG 10,000, 0.2 M NaCl, 10% glycerol, 3% dioxane
|
Resolution 2.85 Å R-free 0.250 |
| 5JNE E2-SUMO-Siz1 E3-SUMO-PCNA complex Deposited 2016-04-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
20–98（79 aa）
Fragment：unp residues 167-445
Chain G
19–98（80 aa）
|
Mutation：Siz1 C361D, Smt3 Delta N-terminus 1-18 Mutation：N-terminal 1-18 delete, K19R | ZN ZINC ION × 1 GOL GLYCEROL × 4 6LN ethane-1,2-dithiol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1 M Tris-HCl (pH 8.5), 5% PEG 10,000, 0.2 M NaCl, 10% glycerol, 3% dioxane
|
Resolution 2.85 Å R-free 0.250 |
| 5KLX Crystal Structure of SMT Fusion Peptidyl-Prolyl Cis-Trans Isomerase from Burkholderia Pseudomallei Complexed with SF110 Deposited 2016-06-26 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–98（86 aa）
Fragment：UNP Q12306 residues 13-98,UNP Q3JK38 residues 2-113
|
Not recorded | 6UO 2-[(2~{S})-1-(phenylmethyl)sulfonylpiperidin-2-yl]carbonyloxyethyl pyridine-3-carboxylate × 1 MG MAGNESIUM ION × 1 IMD IMIDAZOLE × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；BUPSA.00130.A.D21 (CID4597, SMT TAG ON, BATCH 1264062) AT 10.37MG/ML (IN 25MM TRIS, PH8.0, 200MM NACL, 1% GLYCEROL, 1MM TCEP BUFFER) WAS INCUBATED WITH 2MM SF110_S (BSI5665). CRYSTALS WERE PRODUCED BY SITTING DROP VAPOR IFFUSION WITH AN EQUAL VOLUME COMBINATION OF THE PROTEIN/LIGAND COMPLEX AND A SOLUTION CONTAINING 10% W/V PEG20,000, 20% V/V PEG MME 550, 0.03M MGCL2, 0.03M CACL2, 0.1M MES/IMIDAZOLE, PH6.5 (MORPHEUS A1). CRYSTAL TRACKING ID 273103A1, RVA0-10, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
|
Resolution 2.45 Å R-free 0.256 |
| 5KLX Crystal Structure of SMT Fusion Peptidyl-Prolyl Cis-Trans Isomerase from Burkholderia Pseudomallei Complexed with SF110 Deposited 2016-06-26 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–98（86 aa）
Fragment：UNP Q12306 residues 13-98,UNP Q3JK38 residues 2-113
|
Not recorded | 6UO 2-[(2~{S})-1-(phenylmethyl)sulfonylpiperidin-2-yl]carbonyloxyethyl pyridine-3-carboxylate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；BUPSA.00130.A.D21 (CID4597, SMT TAG ON, BATCH 1264062) AT 10.37MG/ML (IN 25MM TRIS, PH8.0, 200MM NACL, 1% GLYCEROL, 1MM TCEP BUFFER) WAS INCUBATED WITH 2MM SF110_S (BSI5665). CRYSTALS WERE PRODUCED BY SITTING DROP VAPOR IFFUSION WITH AN EQUAL VOLUME COMBINATION OF THE PROTEIN/LIGAND COMPLEX AND A SOLUTION CONTAINING 10% W/V PEG20,000, 20% V/V PEG MME 550, 0.03M MGCL2, 0.03M CACL2, 0.1M MES/IMIDAZOLE, PH6.5 (MORPHEUS A1). CRYSTAL TRACKING ID 273103A1, RVA0-10, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
|
Resolution 2.45 Å R-free 0.256 |
| 5KLX Crystal Structure of SMT Fusion Peptidyl-Prolyl Cis-Trans Isomerase from Burkholderia Pseudomallei Complexed with SF110 Deposited 2016-06-26 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
13–98（86 aa）
Fragment：UNP Q12306 residues 13-98,UNP Q3JK38 residues 2-113
|
Not recorded | 6UO 2-[(2~{S})-1-(phenylmethyl)sulfonylpiperidin-2-yl]carbonyloxyethyl pyridine-3-carboxylate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；BUPSA.00130.A.D21 (CID4597, SMT TAG ON, BATCH 1264062) AT 10.37MG/ML (IN 25MM TRIS, PH8.0, 200MM NACL, 1% GLYCEROL, 1MM TCEP BUFFER) WAS INCUBATED WITH 2MM SF110_S (BSI5665). CRYSTALS WERE PRODUCED BY SITTING DROP VAPOR IFFUSION WITH AN EQUAL VOLUME COMBINATION OF THE PROTEIN/LIGAND COMPLEX AND A SOLUTION CONTAINING 10% W/V PEG20,000, 20% V/V PEG MME 550, 0.03M MGCL2, 0.03M CACL2, 0.1M MES/IMIDAZOLE, PH6.5 (MORPHEUS A1). CRYSTAL TRACKING ID 273103A1, RVA0-10, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
|
Resolution 2.45 Å R-free 0.256 |
| 5KLX Crystal Structure of SMT Fusion Peptidyl-Prolyl Cis-Trans Isomerase from Burkholderia Pseudomallei Complexed with SF110 Deposited 2016-06-26 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
13–98（86 aa）
Fragment：UNP Q12306 residues 13-98,UNP Q3JK38 residues 2-113
|
Not recorded | 6UO 2-[(2~{S})-1-(phenylmethyl)sulfonylpiperidin-2-yl]carbonyloxyethyl pyridine-3-carboxylate × 1 MG MAGNESIUM ION × 1 IMD IMIDAZOLE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；BUPSA.00130.A.D21 (CID4597, SMT TAG ON, BATCH 1264062) AT 10.37MG/ML (IN 25MM TRIS, PH8.0, 200MM NACL, 1% GLYCEROL, 1MM TCEP BUFFER) WAS INCUBATED WITH 2MM SF110_S (BSI5665). CRYSTALS WERE PRODUCED BY SITTING DROP VAPOR IFFUSION WITH AN EQUAL VOLUME COMBINATION OF THE PROTEIN/LIGAND COMPLEX AND A SOLUTION CONTAINING 10% W/V PEG20,000, 20% V/V PEG MME 550, 0.03M MGCL2, 0.03M CACL2, 0.1M MES/IMIDAZOLE, PH6.5 (MORPHEUS A1). CRYSTAL TRACKING ID 273103A1, RVA0-10, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
|
Resolution 2.45 Å R-free 0.256 |
| 5V8T Crystal structure of SMT fusion Peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei complexed with SF354 Deposited 2017-03-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–97（85 aa）
Fragment：unp residues 13-97; unp residues 2-113
|
Not recorded | 8ZV 2-{[3,5-bis(2-methoxyethoxy)benzene-1-carbonyl]amino}ethyl (2S)-1-(benzylsulfonyl)piperidine-2-carboxylate × 1 FMT FORMIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；BupsA.00130.a.D21 (CID4597, SMT tag on, Batch 776103) at 10.37mg/ml (in 25mM Tris, pH8.0, 200mM NaCl, 1% glycerol, 1mM TCEP buffer) was incubated with 2mM SF354 (BSI5672). Crystals were produced by sitting drop vapor diffusion with an equal volume combination of the protein/ligand complex and a solution containing 24.55% (w/v) PEG-3350, 50 mM ammonium formate (JCSG_A8 opt screen d7) and cryoprotected with 15% ethylene glycol. Crystal Tracking ID 274545d7, uxe3-7
|
Resolution 2.10 Å R-free 0.221 |
| 5V8T Crystal structure of SMT fusion Peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei complexed with SF354 Deposited 2017-03-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–97（85 aa）
Fragment：unp residues 13-97; unp residues 2-113
|
Not recorded | 8ZV 2-{[3,5-bis(2-methoxyethoxy)benzene-1-carbonyl]amino}ethyl (2S)-1-(benzylsulfonyl)piperidine-2-carboxylate × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；289 K；BupsA.00130.a.D21 (CID4597, SMT tag on, Batch 776103) at 10.37mg/ml (in 25mM Tris, pH8.0, 200mM NaCl, 1% glycerol, 1mM TCEP buffer) was incubated with 2mM SF354 (BSI5672). Crystals were produced by sitting drop vapor diffusion with an equal volume combination of the protein/ligand complex and a solution containing 24.55% (w/v) PEG-3350, 50 mM ammonium formate (JCSG_A8 opt screen d7) and cryoprotected with 15% ethylene glycol. Crystal Tracking ID 274545d7, uxe3-7
|
Resolution 2.10 Å R-free 0.221 |
| 5YC2 Crystal structure of inner membrane protein Bqt4 in complex with telomeric protein Rap1 Deposited 2017-09-06 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
20–92（73 aa）
|
Mutation：Q61E | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1M HEPES sodium pH 7.5, 10% v/v 2-Propanol, 20% w/v Polyethyleneglycol 4000.
|
Resolution 2.70 Å R-free 0.249 |
| 5YC2 Crystal structure of inner membrane protein Bqt4 in complex with telomeric protein Rap1 Deposited 2017-09-06 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
20–92（73 aa）
|
Mutation：Q61E | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1M HEPES sodium pH 7.5, 10% v/v 2-Propanol, 20% w/v Polyethyleneglycol 4000.
|
Resolution 2.70 Å R-free 0.249 |
| 5YCA Crystal structure of inner membrane protein Bqt4 in complex with LEM2 Deposited 2017-09-07 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
20–92（73 aa）
|
Mutation：Q61E | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；289 K；1600 mM Sodium citrate tribasic
|
Resolution 1.57 Å R-free 0.214 |
| 6CFP CRYSTAL STRUCTURE OF POLYMERASE ACID PROTEIN (PA) FROM INFLUENZA A VIRUS, WILSON-SMITH/1933 (H1N1) BOUND TO FRAGMENT HIT BSI-70565 1-{1-[4-FLUOROPHENYL)METHYL]-2-METHYL-1H-IMIDAZOL-4-YL}ETHAN-1-ONE Deposited 2018-02-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–98（86 aa）
|
Not recorded | EZS 1-{1-[(4-fluorophenyl)methyl]-2-methyl-1H-imidazol-4-yl}ethan-1-one × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；MOLECULAR DIMENSIONS MORPHEUS
SCREEN D10: 10% PEG 8000, 20% ETHYLENE GLYCOL; 20MM OF EACH 1,
6-HEXANEDIOL, 1-BUTANOL, 1,2-PROPANEDIOL, 2-PROPANOL, 1,4-
BUTANEDIOL, 1,3-PROPANEDIOL; 100MM TRIS/BICINE PH 8.5;
INVAA.07057.A.D15. AT 20.0 MG/ML, OVERNIGHT SOAK WITH 7 MM
BSI70565, DIRECT CRYO; tray 297881d10, puck WXU6-7
|
Resolution 2.45 Å R-free 0.231 |
| 6O49 CRYSTAL STRUCTURE OF SMT FUSION PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FROM BURKHOLDERIA PSEUDOMALLEI COMPLEXED WITH SF339 Deposited 2019-02-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–98（86 aa）
|
Not recorded | LL7 (2~{S})-~{N}-[3-oxidanylidene-3-[(3,4,5-trimethoxyphenyl)amino]propyl]-1-(phenylmethyl)sulfonyl-piperidine-2-carboxamide × 1 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；289 K；BupsA.00130.a.D21 (CID4597, SMT tag on, Batch 1264062) at 10.37mg/ml (in 25mM Tris, pH8.0, 200mM NaCl, 1% glycerol, 1mM TCEP buffer) was incubated with 2mM SF339_S (BSI5671). Crystals were produced by sitting drop vapor diffusion with an equal volume combination of the protein/ligand complex and a solution containing 100 mM MES pH 6.0, 200 mM Calcium chloride dehydrate, 20% PEG6000 (PACT B11). Crystal Tracking ID 297348b11, izs6-2
|
Resolution 1.85 Å R-free 0.211 |
| 6O49 CRYSTAL STRUCTURE OF SMT FUSION PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FROM BURKHOLDERIA PSEUDOMALLEI COMPLEXED WITH SF339 Deposited 2019-02-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–98（86 aa）
|
Not recorded | LL7 (2~{S})-~{N}-[3-oxidanylidene-3-[(3,4,5-trimethoxyphenyl)amino]propyl]-1-(phenylmethyl)sulfonyl-piperidine-2-carboxamide × 1 CA CALCIUM ION × 1 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；289 K；BupsA.00130.a.D21 (CID4597, SMT tag on, Batch 1264062) at 10.37mg/ml (in 25mM Tris, pH8.0, 200mM NaCl, 1% glycerol, 1mM TCEP buffer) was incubated with 2mM SF339_S (BSI5671). Crystals were produced by sitting drop vapor diffusion with an equal volume combination of the protein/ligand complex and a solution containing 100 mM MES pH 6.0, 200 mM Calcium chloride dehydrate, 20% PEG6000 (PACT B11). Crystal Tracking ID 297348b11, izs6-2
|
Resolution 1.85 Å R-free 0.211 |
| 6O4A CRYSTAL STRUCTURE OF SMT FUSION PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FROM BURKHOLDERIA PSEUDOMALLEI COMPLEXED WITH SF355 Deposited 2019-02-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–98（86 aa）
|
Not recorded | CA CALCIUM ION × 1 LLD 2-(pyridin-3-ylcarbonylamino)ethyl (2~{S})-1-(phenylmethyl)sulfonylpiperidine-2-carboxylate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；BupsA.00130.a.D21 (CID4597, SMT tag on, Batch 1264062) at 10.37mg/ml (in 25mM Tris, pH8.0, 200mM NaCl, 1% glycerol, 1mM TCEP buffer) was incubated with 2mM SF355 (BSI5667). Crystals were produced by sitting drop vapor diffusion with an equal volume combination of the protein/ligand complex and a solution containing HamptonResearch PACT screen (B4): 25% PEG 1500, 100m MIB pH 7.0. The sample was cryoprotected with 15% ethylene glycol: Crystal tray ID 290655b4, puck ID PWP0-3
|
Resolution 2.10 Å R-free 0.208 |
| 6O4A CRYSTAL STRUCTURE OF SMT FUSION PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FROM BURKHOLDERIA PSEUDOMALLEI COMPLEXED WITH SF355 Deposited 2019-02-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
13–98（86 aa）
|
Not recorded | LLD 2-(pyridin-3-ylcarbonylamino)ethyl (2~{S})-1-(phenylmethyl)sulfonylpiperidine-2-carboxylate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；BupsA.00130.a.D21 (CID4597, SMT tag on, Batch 1264062) at 10.37mg/ml (in 25mM Tris, pH8.0, 200mM NaCl, 1% glycerol, 1mM TCEP buffer) was incubated with 2mM SF355 (BSI5667). Crystals were produced by sitting drop vapor diffusion with an equal volume combination of the protein/ligand complex and a solution containing HamptonResearch PACT screen (B4): 25% PEG 1500, 100m MIB pH 7.0. The sample was cryoprotected with 15% ethylene glycol: Crystal tray ID 290655b4, puck ID PWP0-3
|
Resolution 2.10 Å R-free 0.208 |
| 6O4A CRYSTAL STRUCTURE OF SMT FUSION PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FROM BURKHOLDERIA PSEUDOMALLEI COMPLEXED WITH SF355 Deposited 2019-02-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
13–98（86 aa）
|
Not recorded | CA CALCIUM ION × 1 LLD 2-(pyridin-3-ylcarbonylamino)ethyl (2~{S})-1-(phenylmethyl)sulfonylpiperidine-2-carboxylate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；BupsA.00130.a.D21 (CID4597, SMT tag on, Batch 1264062) at 10.37mg/ml (in 25mM Tris, pH8.0, 200mM NaCl, 1% glycerol, 1mM TCEP buffer) was incubated with 2mM SF355 (BSI5667). Crystals were produced by sitting drop vapor diffusion with an equal volume combination of the protein/ligand complex and a solution containing HamptonResearch PACT screen (B4): 25% PEG 1500, 100m MIB pH 7.0. The sample was cryoprotected with 15% ethylene glycol: Crystal tray ID 290655b4, puck ID PWP0-3
|
Resolution 2.10 Å R-free 0.208 |
| 6O4A CRYSTAL STRUCTURE OF SMT FUSION PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FROM BURKHOLDERIA PSEUDOMALLEI COMPLEXED WITH SF355 Deposited 2019-02-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
13–98（86 aa）
|
Not recorded | LLD 2-(pyridin-3-ylcarbonylamino)ethyl (2~{S})-1-(phenylmethyl)sulfonylpiperidine-2-carboxylate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；BupsA.00130.a.D21 (CID4597, SMT tag on, Batch 1264062) at 10.37mg/ml (in 25mM Tris, pH8.0, 200mM NaCl, 1% glycerol, 1mM TCEP buffer) was incubated with 2mM SF355 (BSI5667). Crystals were produced by sitting drop vapor diffusion with an equal volume combination of the protein/ligand complex and a solution containing HamptonResearch PACT screen (B4): 25% PEG 1500, 100m MIB pH 7.0. The sample was cryoprotected with 15% ethylene glycol: Crystal tray ID 290655b4, puck ID PWP0-3
|
Resolution 2.10 Å R-free 0.208 |
| 6P81 Structure of DNA polymerase III, beta subunit/ beta sliding clamp from Klebsiella pneumoniae, expressed with an N-terminal His-Smt3 fusion tag, in complex with Griselimycin Deposited 2019-06-06 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
13–98（86 aa）
Fragment：KlpnA.17987.a.EN11
|
Not recorded | CA CALCIUM ION × 1 PG5 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE × 1 ACT ACETATE ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.5；290 K；Microlytic MCSG-2, condition D4: 30% (V/V) PEG 300, 200mM Calcium acetate, 100mM sodium acetate / acetic acid pH 4.5:
KlpnA.17987.a.EN11.PD383542 at 20.95mg/ml + 2mM griselimycin: tray 309729 D4: cryo: direct: puck ECJ6-1.
|
Resolution 1.75 Å R-free 0.213 |
| 6Q2S Cryo-EM structure of RET/GFRa3/ARTN extracellular complex. The 3D refinement was applied with C2 symmetry. Deposited 2019-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–98（98 aa）
Chain B
1–98（98 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 CA CALCIUM ION × 8 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 6RPQ Crystal structure of PhoCDC21-1 intein Deposited 2019-05-14 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–98（97 aa）
|
Mutation：A101T, C112A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；tri-ammonium citrate
|
Resolution 2.65 Å R-free 0.235 |
| 6UKM STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Compound MSA-2 Deposited 2019-10-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
2–98（97 aa）
|
Mutation：G230A,R293Q | QAD 4-(5,6-dimethoxy-1-benzothiophen-2-yl)-4-oxobutanoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.5；298 K；25% PEG 6000, 100 mM Tris, 200 mM NaCl, 2 mM DTT
|
Resolution 1.74 Å R-free 0.192 |
| 6UKU STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Compound 3 Deposited 2019-10-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
2–98（97 aa）
|
Mutation：G230A,R293Q | QAV 4,4'-[propane-1,3-diylbis(6-methoxy-1-benzothiene-5,2-diyl)]bis(4-oxobutanoic acid) × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.5；298 K；25% PEG 6000, 100 mM Tris, 200 mM NaCl, 2 mM DTT
|
Resolution 1.68 Å R-free 0.221 |
| 6UKV STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Compound 9 Deposited 2019-10-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
2–98（97 aa）
Chain B
2–98（97 aa）
|
Mutation：G230A,R293Q Mutation：G230A,R293Q | QB1 4-[6-(3-{[2-(3-carboxypropanoyl)-6-methoxy-1-benzothiophen-5-yl]oxy}propoxy)-5-methoxy-1-benzothiophen-2-yl]-4-oxobutanoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.5；298 K；25% PEG 6000, 100 mM Tris, 200 mM NaCl, 2 mM DTT
|
Resolution 1.83 Å R-free 0.208 |
| 6UKW STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Compound 10 Deposited 2019-10-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
2–98（97 aa）
Chain B
2–98（97 aa）
|
Mutation：G230A,R293Q Mutation：G230A,R293Q | QB7 4-[6-(3-{[2-(3-carboxypropanoyl)-4-fluoro-6-methoxy-1-benzothiophen-5-yl]oxy}propoxy)-5-methoxy-1-benzothiophen-2-yl]-4-oxobutanoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.5；298 K；25% PEG 6000, 100 mM Tris, 200 mM NaCl, 2 mM DTT
|
Resolution 1.97 Å R-free 0.241 |
| 6UKX STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Compound 11 Deposited 2019-10-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
2–98（97 aa）
Chain B
2–98（97 aa）
|
Mutation：G230A,R293Q Mutation：G230A,R293Q | QBA 4,4'-{propane-1,3-diylbis[oxy(5-methoxy-1-benzothiene-6,2-diyl)]}bis(4-oxobutanoic acid) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.5；298 K；25% PEG 6000, 100 mM Tris, 200 mM NaCl, 2 mM DTT
|
Resolution 1.93 Å R-free 0.217 |
| 6UKY STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Compound 12 Deposited 2019-10-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
2–98（97 aa）
|
Mutation：G230A,R293Q | QBD 4-(6-{3-[2-(3-carboxypropanoyl)-6-methoxy-1-benzothiophen-4-yl]propyl}-5-methoxy-1-benzothiophen-2-yl)-4-oxobutanoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.5；298 K；25% PEG 6000, 100 mM Tris, 200 mM NaCl, 2 mM DTT
|
Resolution 1.95 Å R-free 0.227 |
| 6UKZ STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Compound 6 Deposited 2019-10-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
2–98（97 aa）
Chain B
2–98（97 aa）
|
Mutation：G230A,R293Q Mutation：G230A,R293Q | QBG 4-[5-(2-{[2-(3-carboxypropanoyl)-4-fluoro-6-methoxy-1-benzothiophen-5-yl]oxy}ethoxy)-6-methoxy-1-benzothiophen-2-yl]-4-oxobutanoic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.5；298 K；25% PEG 6000, 100 mM Tris, 200 mM NaCl, 2 mM DTT
|
Resolution 1.52 Å R-free 0.213 |
| 6UL0 STING C-terminal Domain Complexed with Non-cyclic Dinucleotide Compound 4 Deposited 2019-10-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
2–98（97 aa）
|
Mutation：G230A,R293Q | QBJ 4-{5-[(1Z)-3-{[2-(3-carboxypropanoyl)-6-methoxy-1-benzothiophen-5-yl]oxy}prop-1-en-1-yl]-6-methoxy-1-benzothiophen-2-yl}-4-oxobutanoic acid × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.5；298 K；25% PEG 6000, 100 mM Tris, 200 mM NaCl, 2 mM DTT
|
Resolution 1.76 Å R-free 0.242 |
| 6VEL Crystal Structure of Human E-cadherin bound by mouse monoclonal antibody 66E8Fab Deposited 2020-01-02 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1–98（98 aa）
|
Not recorded | SO4 SULFATE ION × 6 CA CALCIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；A complex of HosaA.19747.a.KW2, MumuA.20194.a.LG23, and MumuA.20195.a.LH23 was crystallized at 10.4 mg/ml at 14C and mixed 1:1 with 12.5% (w/v) PEG 4000, 20% (v/v) 1,2,6-hexanetriol, 0.1M GlyGly/AMPD pH 8.5, 0.03M of each Lithium sulfate, Sodium sulfate, and Potassium sulfate. Tray 307437a10: puck ckt8-9.
|
Resolution 2.65 Å R-free 0.236 |
| 6VW2 Cryo-EM structure of human islet amyloid polypeptide (hIAPP, or amylin) fibrils Deposited 2020-02-18 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 10 PDB declaration: decameric |
Chain A
1–97（97 aa）
Chain B
1–97（97 aa）
Chain C
1–97（97 aa）
Chain D
1–97（97 aa）
Chain E
1–97（97 aa）
Chain F
1–97（97 aa）
Chain G
1–97（97 aa）
Chain H
1–97（97 aa）
Chain I
1–97（97 aa）
Chain J
1–97（97 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7LTO Nse5-6 complex Deposited 2021-02-19 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–98（98 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7O2W Structure of the C9orf72-SMCR8 complex Deposited 2021-03-31 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–96（95 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7P47 Structure of the E3 ligase Smc5/Nse2 in complex with Ubc9-SUMO thioester mimetic Deposited 2021-07-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain D
1–98（98 aa）
Chain E
1–98（98 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；311 K；12% PEG8000, 0.2M dimethyl-2-hydroxyethylammoniumpropane sulfonate (NDSB 211), 8% ethylene glycol, 0.1M MES pH 6.5
|
Resolution 3.31 Å R-free 0.293 |
| 7P7I Native structure of N-acetylglucosamine kinase from Plesiomonas shigelloides Deposited 2021-07-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain AAA
2–96（95 aa）
Chain BBB
2–96（95 aa）
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 ZN ZINC ION × 2 PGE TRIETHYLENE GLYCOL × 2 EDO 1,2-ETHANEDIOL × 8 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；291 K；60 mM divalent cations; 0.1 M Tris/bicine pH 8.5; 12.5% each MPD, PEG 1K, PEG 3350.
condition A12 from Morpheus screen (Molecular Dimensions)
|
Resolution 1.70 Å R-free 0.210 |
| 7P7W N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine and ADP Deposited 2021-07-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain AAA
2–96（95 aa）
Chain BBB
2–96（95 aa）
|
Not recorded | ADP ADENOSINE-5'-DIPHOSPHATE × 2 GOL GLYCEROL × 3 IMD IMIDAZOLE × 4 NDG 2-acetamido-2-deoxy-alpha-D-glucopyranose × 2 ZN ZINC ION × 4 EDO 1,2-ETHANEDIOL × 17 PEG DI(HYDROXYETHYL)ETHER × 1 K POTASSIUM ION × 2 IPA ISOPROPYL ALCOHOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；291 K；120 mM alcohols; ; 0.1 M imidazole/MES pH 6.5; 30% each glycerol and PEG 4K
Condition A3 of Morpheus screen (Molecular dimensions). Crystal was soaked for 60 seconds in cryoprotectant containing 10 mM
ADP
|
Resolution 1.57 Å R-free 0.211 |
| 7P9L N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine-6-phosphate Deposited 2021-07-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain AAA
2–96（95 aa）
Chain BBB
2–96（95 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 22 PEG DI(HYDROXYETHYL)ETHER × 7 4QY 2-acetamido-2-deoxy-6-O-phosphono-beta-D-glucopyranose × 2 ZN ZINC ION × 4 K POTASSIUM ION × 2 PO4 PHOSPHATE ION × 2 CL CHLORIDE ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；291 K；90 mM halogens; 0.1 M Tris/bicine pH 8.5; 30% each PEG 550 MME and PEG 20K,
condition B9 from Morpheus screen (Molecular Dimensions)
|
Resolution 1.75 Å R-free 0.223 |
| 7P9P N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine and AMP-PNP inhibitor Deposited 2021-07-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain AAA
2–96（95 aa）
Chain BBB
2–96（95 aa）
|
Not recorded | ZN ZINC ION × 4 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 PEG DI(HYDROXYETHYL)ETHER × 3 PGE TRIETHYLENE GLYCOL × 2 NDG 2-acetamido-2-deoxy-alpha-D-glucopyranose × 2 EDO 1,2-ETHANEDIOL × 15 K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；291 K；60 mM divalent cations; 0.1 M imidazole/MES pH 6.5; 30% each glycerol and PEG 4K. Condition A3 from Morpheus screen (Molecular Dimensions)
|
Resolution 2.11 Å R-free 0.233 |
| 7P9Y N-acetylglucosamine kinase from Plesiomonas shigelloides compexed with alpha-N-acetylglucosamine Deposited 2021-07-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain AAA
2–96（95 aa）
Chain BBB
2–96（95 aa）
|
Not recorded | MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 3 EDO 1,2-ETHANEDIOL × 16 PGE TRIETHYLENE GLYCOL × 1 NDG 2-acetamido-2-deoxy-alpha-D-glucopyranose × 2 ZN ZINC ION × 4 K POTASSIUM ION × 2 CL CHLORIDE ION × 2 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；291 K；90 mM halogens; 0.1 M Na-HEPES/MOPS pH 7.5; 12.5% each MPD, PEG 1K, PEG 3350
Condition B8 of Morpheus screen (Molecular Dimensions)
|
Resolution 1.94 Å R-free 0.250 |
| 7PA1 Structure of N-acetylglucosamine kinase from Plesiomonas shigelloides in complex with AMP-PNP in the absence of N-acetylglucoseamine substrate Deposited 2021-07-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain AAA
2–96（95 aa）
Chain BBB
2–96（95 aa）
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 ZN ZINC ION × 2 PGE TRIETHYLENE GLYCOL × 4 EDO 1,2-ETHANEDIOL × 9 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；291 K；0.09M NPS; 0.1 M Tris/bicine pH 8.5; 30% each PEG 550 MME and PEG 20K, condition C9 from Morpheus crystallisation screen (Molecular Dimensions).
|
Resolution 2.20 Å R-free 0.252 |
| 7SDE Cryo-EM structure of Nse5/6 heterodimer Deposited 2021-09-29 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–98（98 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7ZHS 3D reconstruction of the cylindrical assembly of DnaJA2 delta G/F by imposing D5 symmetry Deposited 2022-04-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 40 PDB declaration: 40-meric |
Chain A
3–98（96 aa）
Chain B
3–98（96 aa）
Chain C
3–98（96 aa）
Chain D
3–98（96 aa）
Chain E
3–98（96 aa）
Chain F
3–98（96 aa）
Chain G
3–98（96 aa）
Chain H
3–98（96 aa）
Chain I
3–98（96 aa）
Chain J
3–98（96 aa）
Chain K
3–98（96 aa）
Chain L
3–98（96 aa）
Chain M
3–98（96 aa）
Chain N
3–98（96 aa）
Chain O
3–98（96 aa）
Chain P
3–98（96 aa）
Chain Q
3–98（96 aa）
Chain R
3–98（96 aa）
Chain S
3–98（96 aa）
Chain T
3–98（96 aa）
Chain U
3–98（96 aa）
Chain V
3–98（96 aa）
Chain W
3–98（96 aa）
Chain X
3–98（96 aa）
Chain Y
3–98（96 aa）
Chain Z
3–98（96 aa）
Chain a
3–98（96 aa）
Chain b
3–98（96 aa）
Chain c
3–98（96 aa）
Chain d
3–98（96 aa）
Chain e
3–98（96 aa）
Chain f
3–98（96 aa）
Chain g
3–98（96 aa）
Chain h
3–98（96 aa）
Chain i
3–98（96 aa）
Chain j
3–98（96 aa）
Chain k
3–98（96 aa）
Chain l
3–98（96 aa）
Chain m
3–98（96 aa）
Chain n
3–98（96 aa）
|
Not recorded | ZN ZINC ION × 80 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.90 Å |
| 7ZWL Crystal structure of human STING in complex with 3',3'-c-di-(2'F,2'd<carba>AMP) Deposited 2022-05-19 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
2–98（97 aa）
|
Not recorded | K43 9-[(1~{R},6~{R},8~{R},9~{S},10~{R},15~{R},17~{R},18~{S})-17-(6-aminopurin-9-yl)-9,18-bis(fluoranyl)-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,11,13-tetraoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.3.0.0^{6,10}]octadecan-8-yl]purin-6-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Lithium acetate,
20% (w/v) PEG 3350
|
Resolution 2.00 Å R-free 0.249 |
| 8B7F Nuclease from C. glutamicum Deposited 2022-09-29 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
2–98（97 aa）
Chain B
2–98（97 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；10% (w/v) PEG 6K, 30% (v/v) ethanol and 10 mM sodium acetate
|
Resolution 4.60 Å R-free 0.311 |
| 8DMB Structure of Desulfovirgula thermocuniculi IsrB (DtIsrB) in complex with omega RNA and target DNA Deposited 2022-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: tetrameric |
Chain P
1–98（98 aa）
|
Mutation：H584L | MG MAGNESIUM ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8R1F Monomeric E6AP-E6-p53 ternary complex Deposited 2023-11-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–98（98 aa）
|
Mutation：C80S,C97S,C111S,C140S | ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.67 Å |
| 8R1G Dimeric ternary structure of E6AP-E6-p53 Deposited 2023-11-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain B
1–98（98 aa）
Chain E
1–98（98 aa）
|
Mutation：C80S,C97S,C111S,C140S Mutation：C80S,C97S,C111S,C140S | ZN ZINC ION × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.99 Å |
| 8UZH SUMO fused Trehalose Synthase (TreS) of Mycobacterium tuberculosis Deposited 2023-11-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
2–98（97 aa）
Chain B
2–98（97 aa）
|
Not recorded | CA CALCIUM ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；0.8 M Ammonium sulfate, 0.1 M Sodium Citrate pH 5.0
|
Resolution 2.80 Å R-free 0.290 |
| 8VQH CryoEM structure of BchN-BchB electron acceptor component protein of DPOR Deposited 2024-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–96（96 aa）
Chain D
1–96（96 aa）
|
Not recorded | SF4 IRON/SULFUR CLUSTER × 2 CU COPPER (II) ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 8X7V Structure of human SCMC ternary complex Deposited 2023-11-26 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1–98（98 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.01 Å |
| 8X7W Structure of dimeric human SCMC complex Deposited 2023-11-26 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain C
1–98（98 aa）
Chain F
1–98（98 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.36 Å |
| 9E7U Cryo-EM structure of NOT1:NOT8:PieF Deposited 2024-11-04 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1–95（95 aa）
|
Not recorded | MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 9E7V Off-pathway Mycobacterium tuberculosis transcription initiation promoter complex (RNA Polymerase with Sigma-A, CarD, and RbpA) Deposited 2024-11-04 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric |
Chain M
1–98（98 aa）
|
Not recorded | POP PYROPHOSPHATE 2- × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9E7Y De Novo Mycobacterium tuberculosis transcription initiation promoter complex with 7-mer RNA and disordered Beta' Lid element (RNA Polymerase with Sigma-A, CarD, and RbpA) Deposited 2024-11-04 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: undecameric |
Chain M
1–98（98 aa）
|
Not recorded | POP PYROPHOSPHATE 2- × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 9E84 De Novo Mycobacterium tuberculosis transcription initiation promoter complex with 6-mer RNA and disordered Sigma-A region 4 domain (RNA Polymerase with Sigma-A, CarD, and RbpA) Deposited 2024-11-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: 11-meric |
Chain M
1–98（98 aa）
|
Not recorded | POP PYROPHOSPHATE 2- × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 9E85 De Novo Mycobacterium tuberculosis transcription initiation promoter complex with 6-mer RNA and closed Beta' clamp (RNA Polymerase with Sigma-A, CarD, and RbpA) Deposited 2024-11-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: 11-meric |
Chain M
1–98（98 aa）
|
Not recorded | POP PYROPHOSPHATE 2- × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9E86 De Novo Mycobacterium tuberculosis transcription initiation promoter complex with 5-mer RNA and open Beta' clamp (RNA Polymerase with Sigma-A, CarD, and RbpA) Deposited 2024-11-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: 11-meric |
Chain M
1–98（98 aa）
|
Not recorded | POP PYROPHOSPHATE 2- × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 9E87 De Novo Mycobacterium tuberculosis transcription initiation pre-RPO promoter complex with open Beta' clamp (RNA Polymerase with Sigma-A, CarD, and RbpA) Deposited 2024-11-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: decameric |
Chain M
1–98（98 aa）
|
Not recorded | ZN ZINC ION × 2 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 9E88 De novo backtracked transcription elongation complex of Mycobacterium tuberculosis RNA polymerase on a linear DNA fragment (TEC-Backtracked) Deposited 2024-11-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: nonameric |
Chain M
1–98（98 aa）
|
Not recorded | ZN ZINC ION × 2 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9G8I Sumo-Darpin-A10-complex Deposited 2024-07-23 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
21–95（75 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Bis-Tris pH 6.5, 23% (v/v) PEG 3350
|
Resolution 2.51 Å R-free 0.301 |
| 9G8I Sumo-Darpin-A10-complex Deposited 2024-07-23 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
21–95（75 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Bis-Tris pH 6.5, 23% (v/v) PEG 3350
|
Resolution 2.51 Å R-free 0.301 |
| 9GAU Sumo-Darpin-C10-complex Deposited 2024-07-29 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
21–96（76 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M Bis-Tris. 16% (v/v)PEG 3350
|
Resolution 2.64 Å R-free 0.288 |
| 9HDO The Human LINE-1 ORF2p target-primed reverse transcription complex Deposited 2024-11-12 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: heptameric |
Chain A
2–98（97 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 1 D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.30 Å |
| 9HDP The Human LINE-1 ORF2p target-primed reverse transcription complex with the fingers domain in a closed conformation Deposited 2024-11-12 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: heptameric |
Chain A
2–98（97 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 1 D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 9HDQ The Human LINE-1 ORF2p target-primed reverse transcription complex with the fingers domain in an open conformation Deposited 2024-11-12 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: heptameric |
Chain A
2–98（97 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.45 Å |
| 9HDR Human LINE-1 ORF2p target-primed reverse transcription complex with EN domain resolved Deposited 2024-11-12 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: heptameric |
Chain A
2–98（97 aa）
|
Not recorded | MG MAGNESIUM ION × 1 ZN ZINC ION × 1 D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9HX5 Apo structure of SRSF6 RRM2 WT Deposited 2025-01-07 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–98（86 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.1 M Bis-Tris propane pH 8.5, 0.2 M Sodium sulfate, 20 % PEG 3350, 10 % Ethylene glycol
|
Resolution 2.10 Å R-free 0.258 |
| 9HX7 Structure of SRSF6 RRM2 WT with "GGA"-RNA Deposited 2025-01-07 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: dimeric |
Chain A
13–98（86 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M HEPES pH 7.0, 0.1 M NH4SO4, 0.1 M Na-Form, 25 % Smear Broad
|
Resolution 2.30 Å R-free 0.250 |
| 9HX8 Apo structure of SRSF6 RRM2 W123A Deposited 2025-01-07 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
13–98（86 aa）
|
Mutation：W123A | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.1 M Na-Citrate, 20 % PEG 3350
|
Resolution 2.00 Å R-free 0.259 |
| 9IIS GDP-fucose pyrophosphorylase part of FKP with a SUMO tag Deposited 2024-06-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–98（98 aa）
|
Not recorded | EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；PEG 3350, ammonium acetate, HEPES
|
Resolution 2.36 Å R-free 0.254 |
| 9KPZ Structure of TolQRA complex at pH 5.4 from E.coli Deposited 2024-11-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain H
3–99（97 aa）
Chain I
3–99（97 aa）
Chain J
3–99（97 aa）
Chain K
3–99（97 aa）
Chain L
3–99（97 aa）
|
Not recorded | 3PE 1,2-Distearoyl-sn-glycerophosphoethanolamine × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.18 Å |
| 9KQ0 Structure of TolQRA complex at pH 8.0 from E.coli Deposited 2024-11-24 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain H
3–99（97 aa）
Chain I
3–99（97 aa）
Chain J
3–99（97 aa）
Chain K
3–99（97 aa）
Chain L
3–99（97 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 9MB6 Cryo-EM structure of wild-type SaCas9-guide RNA-mismatched target DNA complex Deposited 2025-03-15 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
3–98（96 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.01 Å |
| 9MB7 Cryo-EM structure of eSaCas9-NNG-guide RNA-mismatched target DNA complex Deposited 2025-03-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: tetrameric |
Chain A
3–98（96 aa）
|
Not recorded | MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.88 Å |
| 9OIK Structure of S. Typhimurium 14028 Gifsy-1 prophage HepS bound to bacteriophage lambda J Tail Tip Deposited 2025-05-06 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric |
Chain C
1–98（98 aa）
Chain D
1–98（98 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M Sodium Acetate, 16% PEG 4000, 0.1 M Tris pH 8.5
|
Resolution 1.86 Å R-free 0.209 |
| 9OPR TMPRSS2 S441A in complex with the H1H7 Fab and anti-kappa light chain nanobody Deposited 2025-05-19 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–94（94 aa）
|
Mutation：S441A | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9SMX CM1-activated gTuRC in complex with nascent alpha-E254D mutant microtubules Deposited 2025-09-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 73 PDB declaration: 73-meric |
Chain AC
2–99（98 aa）
Chain CC
2–99（98 aa）
Chain Cc
2–99（98 aa）
Chain EC
2–99（98 aa）
Chain Ec
2–99（98 aa）
Chain GC
2–99（98 aa）
Chain Gc
2–99（98 aa）
Chain MC
2–99（98 aa）
Chain Mc
2–99（98 aa）
|
Not recorded | GTP GUANOSINE-5'-TRIPHOSPHATE × 11 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.67 Å |
| 9SYR Human quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatD Deposited 2025-10-13 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 80 PDB declaration: 86-meric |
Chain Nd
4–98（95 aa）
|
Not recorded | ZN ZINC ION × 10 COA COENZYME A × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.55 Å |
| 9UT1 The helicase-primase complex from HHV1 bound with ssDNA and amenamevir Deposited 2025-05-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: tetrameric |
Chain B
3–98（96 aa）
Chain C
3–98（96 aa）
|
Mutation：R64T/R71E Mutation：R64T/R71E | A1BXD Amenamevir × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.14 Å |
| 9UT3 The helicase module of the helicase-primase complex from HHV1 bound with ssDNA and amenamevir Deposited 2025-05-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: trimeric |
Chain B
3–98（96 aa）
|
Mutation：R64T/R71E | A1BXD Amenamevir × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.88 Å |
| 9UT4 The primase module of the helicase-primase complex from HHV1 bound with ssDNA and amenamevir Deposited 2025-05-02 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
3–98（96 aa）
Chain C
3–98（96 aa）
|
Mutation：R64T/R71E Mutation：R64T/R71E | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.91 Å |
| 9UT5 The helicase-primase complex from HHV1 bound with ssDNA and pritelivir Deposited 2025-05-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: tetrameric |
Chain B
3–98（96 aa）
Chain C
3–98（96 aa）
|
Mutation：R64T/R71E Mutation：R64T/R71E | A1BXB Pritelivir × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.32 Å |
| 9UT6 The helicase module of the helicase-primase complex from HHV1 bound with ssDNA and pritelivir Deposited 2025-05-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: trimeric |
Chain B
3–98（96 aa）
|
Mutation：R64T/R71E | A1BXB Pritelivir × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.12 Å |
| 9UT7 The Primase module of the helicase-primase complex from HHV1 bound with ssDNA and pritelivir Deposited 2025-05-02 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
3–98（96 aa）
Chain C
3–98（96 aa）
|
Mutation：R64T/R71E Mutation：R64T/R71E | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.08 Å |
| 9Z3K SARS-CoV-2 S2 trimer stabilized in the early fusion intermediate conformation by circular permutation and clamping by gp41 (E-FICs-v1) Deposited 2025-11-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–94（94 aa）
Chain B
1–94（94 aa）
Chain C
1–94（94 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
95 other PDB entries and 116 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | SMT3_YEAST |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–101； UniProt 1–101 |
